| title | author | date |
|---|---|---|
Setting up the website |
Joyce Hsiao |
2015-12-12 |
Last updated: r Sys.Date()
Code version: r system("git log -1 --format='%H'", intern = TRUE)
source("chunk-options.R")
Copy an exisiting GitHub repository and use GitHub Pages to produce a website for the repository.
I use ashlar as an example and give a simple tutorial for setting up a website. You don't have to publish this website, but I suggest you do as a practice.
Cloning ashlar
ashlar is set up to mimic the workflow implemented in singleCellSeq. Both projects adopt the popular rmarkdown website layout.
I suggest cloning into a new folder in order to distinguish your work from the example repository.
git clone https://github.com/jhsiao999/ashlar.git ashlar-trial
Remote directory of the clone is still [ashlar][http://github.com/jhsiao999/ashlar]. Make sure you change the name of the remote repository.
git remote rm origin
git remote add origin https://github.com/jhsiao999/ashlar-trial.git
Create a repository at github.com. Then, push content of the entire directory to the master branch. We use git add -f option to force add html files to the master branch, such as index.html for table of content. The default .gitignore in [ashlar][http://github.com/jhsiao999/ashlar] ignores htmls.
git add -f --all
git commit -m "first commit"
git push origin master
Option 1: All content for my eyes only
Open index.html. This is the homepage of your unpubished website. You are DONE!
If you choose this option, you only have the master branch. The default of the master branch is to not push htmls, pngs, pdfs, etc, so edit the .gitignore to add these files when updating the remote directory.
Option 2: Publish it! Keep a two-branch workflow.
Create a branch named gh-pages. GitHub then publishes the content for you.
git checkout -b gh-pages
git add -f --all
git commit -m "Build site"
git push origin gh-pages
Note that since the site is kept under the anaysis folder, your site address is under the analysis directory.
https://jhsiao999.github.io/ashlar-trial/analysis
This two-branch workflow is set up to keep the source files (such as Rmds) separate from the html pages and the output figures. It allows me to keep clean repositories: master for the source, and gh-pages only for the website.
I mostly use RStudio to generate htmls, but when there are a large number of analysis files that need to be updated, I choose to use the simple make command. Below are two of my most recently used paths of update GitHub Pages.
Path 1: I mostly use this one when there's only a small analysis file to be updated.
## Work at the gh-pages branch, push website content to gh-pages,
## push source to the master
git checkout gh-pages
cd analysis
make # (or use knitr to render the Rmds)
git add -f *Rmd *html figure/*
git commit -m "add new analysis"
git push origin gh-pages
git checkout master
git merge gh-pages
git add new-analysis.Rmd index.Rmd
git commit -m "add new analysis"
git push origin master
Path 2: I use this when the site has not been update in a while, and I need to compile a large number of Rmds.
## Work at the master branch, keep all htmls local
## Push source to the master branch, use make to generate htmls
## for the gh-pages branch
git checkout master
cd analysis
git add new-analysis.Rmd index.Rmd
git commit -m "add new analysis"
git push origin master
git checkout gh-pages
git merge master
make
git add *Rmd *html figure/*
git commit -m "add new analysis"
git push origin gh-pages